Modelling networks from sequence to consequence in eukaryotes

Event

March
282011

March
292011

Location

Overview

Organised by Professor Dirk-Jan de Koning and Professor Chris Haley

The projected benefits of systems biology for understanding variation in human disease susceptibility or sustainable agriculture requires a bottom-up integration of research in genetics, statistics, mathematical modelling, bioinformatics and physiology. The meeting will bring together keynote speakers from the intersection of these disciplines who apply ‘systems’ approaches to study complex variation in plants, animals or humans.

DJ received his Masters in Animal Sciences from Wageningen University (NL) in 1996. He was awarded his PHD from Wageningen University in 2001 on the thesis entitled: "Identification of (non-) Mendelian factors affecting pork production". This was followed by a post-doctoral position at The Roslin Institute, Edinburgh, where he became a career track fellow in 2003 followed by promotion to group leader in 2007. In October 2010 he started his current appointment as professor in Animal Breeding and Genetics at The Swedish University of Agricultural sciences in Uppsala, Sweden, where he works full time since January 2011. His main research interest is in unraveling the genetic basis of complex trait with a focus on, but not restricted to, livestock animals. Having searched, and found, genomic regions (so called QTL) affecting economically important traits in a range of species, he realized that genome mapping by itself is insufficient to find causal DNA variants and understand the mechanisms underlying genetic variation. He then became interested in the use of intermediate phenotypes, such as gene expression, to try and unravel what genes or gene pathways are affected by the QTL and thereby providing a short track to potential candidate genes underlying the QTL.Back to list

Professor Chris Haley, MRC Human Genetics Unit, UK

Professor Chris Haley, FRSE holds a joint appointment between the MRC Human Genetics Unit and the Roslin Institute at the University of Edinburgh. He joined Roslin Institute in 1984, subsequently becoming head of the Department of Genetics and Genomics in 1996. In 2008 Professor Haley moved to the MRC Human Genetics Unit within the division of Biomedical Systems Analysis but retains a part time appointment and research programmes at Roslin Institute.

Professor Haley’s interests lie in developing an understanding of the control complex traits, where inter-individual variation within and between populations is controlled by the variation of a number of genes and environmental factors and by the complex interactions of these components. Professor Haley’s research focuses both on developing approaches to dissect complex traits and in applications of these approaches to specific biological models.

Welcome

Whole genomes and epigenomes for dissection of complex traits

Professor Tim Aitman, Imperial College London, UK

Abstract

Tim Aitman is Professor of Clinical and Molecular Genetics at Imperial, Head of the CSC Physiological Genomics and Medicine Group and Research Strategy Lead for Genetics and Genomic Medicine in the Imperial College Faculty of Medicine. He coordinates the Leducq Transatlantic CARDIANET Network of Exellence and was coordinator of the EURATools FP6 Integrated Project for development of functional genomics tools in the rat (2005-10). He is a Fellow of the Royal College of Physicians and Academy of Medical Sciences, is a member of editorial boards of the Journal of Lipid Research and Mammalian Genome and has sat on the British Heart Foundation's Project Grants and Fellowships Committees. His research achievements include the genetic dissection of insulin resistance in rats and humans, the rat work leading to the identification of Cd36 as an insulin resistance gene (Aitman et al 1997, Nature Genet 14:197-201; Aitman et al 1999, Nature Genet 21:76-83; Pravenec et al 2001, Nature Genet 27:156-158). This was one of the first genes identified for any mammalian complex trait, and the first successful integrated use of microarray-based expression profiling with genetic linkage analysis. More recently he has used global expression profiling and linkage analysis to understand better the genes and metabolic pathways leading to the common syndromes of insulin resistance (Hubner et al 2005, Nature Genet 37:243-53) and has identified copy number variation in the Fcgr3 gene as a cause of autoimmunity in rats and humans (Aitman et al 2006, Nature 439:951-5). More recently, he drove the identification of genes for glomerulonephritis and cardiac hypertrophy in rats and humans (Petretto et al 2008, Nature Genet 40: 546-552; Behmoaras et al 2008, Nature Genet. 40: 553-559) and the sequencing of the genome of the spontaneously hypertensive rat, the first mammalian model organism to have been sequenced with next generation sequencing (Atanur et al, 2010. Genome Res 20: 791-803.). His work now continues to explore the genetics and epigenetics of genetically complex phenotypes.

Professor Tim Aitman, Imperial College London, UK

Tim Aitman is Professor of Clinical and Molecular Genetics at Imperial, Head of the CSC Physiological Genomics and Medicine Group and Research Strategy Lead for Genetics and Genomic Medicine in the Imperial College Faculty of Medicine. He coordinatesthe Leducq Transatlantic CARDIANET Network of Exellence and was coordinator of the EURATools FP6 Integrated Project for development of functional genomics tools in the rat (2005-10). He is a Fellow of the Royal College of Physicians and Academy of Medical Sciences, is a member of editorial boards of the Journal of Lipid Research and Mammalian Genome and has sat on the British Heart Foundation's Project Grants and Fellowships Committees. His research achievements include the genetic dissection of insulin resistance in rats and humans, the rat work leading to the identification of Cd36 as an insulin resistance gene (Aitman et al 1997, Nature Genet 14:197-201; Aitman et al 1999, Nature Genet 21:76-83; Pravenec et al 2001, Nature Genet 27:156-158). This was one of the first genes identified for any mammalian complex trait, and the first successful integrated use of microarray-based expression profiling with genetic linkage analysis. More recently he has used global expression profiling and linkage analysis to understand better the genes and metabolic pathways leading to the common syndromes of insulin resistance (Hubner et al 2005, Nature Genet 37:243-53) and has identified copy number variation in the Fcgr3 gene as a cause of autoimmunity in rats and humans (Aitman et al 2006, Nature 439:951-5). More recently, he drove the identification of genes for glomerulonephritis and cardiac hypertrophy in rats and humans (Petretto et al 2008, Nature Genet 40: 546-552; Behmoaras et al 2008, Nature Genet. 40: 553-559) and the sequencing of the genome of the spontaneously hypertensive rat, the first mammalian model organism to have been sequenced with next generation sequencing (Atanur et al, 2010. Genome Res 20: 791-803.). His work now continues to explore the genetics and epigenetics of genetically complex phenotypes.

Reverse enigineering the genotype-phenotype map in C elegans

Dr Matthew Rockman, New York University, USA

Abstract

Matthew Rockman is an assistant professor in the Department of Biology and the Center for Genomics and Systems Biology at New York University. His research centers on the molecular and evolutionary causes of heritable phenotypic variation as a means of understanding the genetic basis of evolutionary change. Rockman received a PhD from Duke for work with Greg Wray on cis-regulatory polymorphism and conducted postdoctoral research with Leonid Kruglyak at Princeton on the genetics of phenotypic variation in C. elegans. His lab at NYU is now working to understand the role that recombination and outcrossing play, in interaction with mutation, selection, and drift, to shape phenotypic diversity. Rockman's work has been supported by Fellowships from the Fulbright Foundation, the US National Science Foundation, and the Jane Coffin Childs Fund. His lab's current work is supported by the US National Institutes of Health, the Ellison Medical Foundation, and the Human Frontier Science Program.

Dr Matthew Rockman, New York University, USA

Matthew Rockman is an assistant professor in the Department of Biology and the Center for Genomics and Systems Biology at New York University. His research centers on the molecular and evolutionary causes of heritable phenotypic variation as a means of understanding the genetic basis of evolutionary change. Rockman received a PhD from Duke for work with Greg Wray on cis-regulatory polymorphism and conducted postdoctoral research with Leonid Kruglyak at Princeton on the genetics of phenotypic variation in C. elegans. His lab at NYU is now working to understand the role that recombination and outcrossing play, in interaction with mutation, selection, and drift, to shape phenotypic diversity. Rockman's work has been supported by Fellowships from the Fulbright Foundation, the US National Science Foundation, and the Jane Coffin Childs Fund. His lab's current work is supported by the US National Institutes of Health, the Ellison Medical Foundation, and the Human Frontier Science Program.

Abstract

Dirk Husmeier graduated in Physics (Dipl.-Phys.) at the University of Bochum (Germany) in 1991, and received both his M.Sc. (Information Processing and Neural Networks) and Ph.D. (Applied Mathematics and Neural Computation) degrees from King’s College London in 1994 and 1997, respectively. After working as a postdoctoral research fellow in the Electrical Engineering Department of Imperial College London from 1997 to 1999, he joined Biomathematics and Statistics Scotland (BioSS) as a research scientist in October 1999. Since 2006, Dr Husmeier has been leading the statistical bioinformatics research theme at BioSS

Dr Dirk Husmeier, Biomathematics and Statistics Scotland, UK

Dirk Husmeier graduated in Physics (Dipl.-Phys.) at the University of Bochum (Germany) in 1991, and received both his M.Sc. (Information Processing and Neural Networks) and Ph.D. (Applied Mathematics and Neural Computation) degrees from King’s College London in 1994 and 1997, respectively. After working as a postdoctoral research fellow in the Electrical Engineering Department of Imperial College London from 1997 to 1999, he joined Biomathematics and Statistics Scotland (BioSS) as a research scientist in October 1999. Since 2006, Dr Husmeier has been leading the statistical bioinformatics research theme at BioSS.

Sparse modelling and inference of dynamic genetic networks

Professor Ernst Wit, Groningen University, The Netherlands

Abstract

Professor Wit is the Chair of Statistics and Probability at the Johann Bernoulli Institute at the University of Groningen since 2008. Before this he held positions at the University of Glasgow and Lancaster University. He obtained his PhD in Philosophy in 1997 from the Pennsylvania State University and a PhD in Statistics in 2000 from the University of Chicago. His research interest focus modelling of structured data, in particular with applications in genomics. He is the author of the book "Statistics for Microarrays" (Wiley 2004) and is currently working on a manuscript on statistical modelling of genetic networks. Recurrent themes in this work are high-dimensional data, sparse and structured models and complex model selection. Ernst Wit is a scientific advisory board member of The Genome Analysis Centre in Norwich.

Professor Ernst Wit, Groningen University, The Netherlands

Professor Wit is the Chair of Statistics and Probability at the Johann Bernoulli Institute at the University of Groningen since 2008. Before this he held positions at the University of Glasgow and Lancaster University. He obtained his PhD in Philosophy in 1997 from the Pennsylvania State University and a PhD in Statistics in 2000 from the University of Chicago. His research interest focus modelling of structured data, in particular with applications in genomics. He is the author of the book "Statistics for Microarrays" (Wiley 2004) and is currently working on a manuscript on statistical modelling of genetic networks. Recurrent themes in this work are high-dimensional data, sparse and structured models and complex model selection. Ernst Wit is a scientific advisory board member of The Genome Analysis Centre in Norwich.

Gene and QTL networks

Dr Lauren McIntyre, University of Florida, USA

Abstract

Lauren McIntyre received her PhD in 1996 from North Carolina State University under the direction of Dr. Bruce Weir. Her PhD focused on testing Hardy-Weinberg Equilibrium. At Duke University Medical School she developed methods for mapping multigenic binary traits. In 1999, with a move to Purdue University, Dr. McIntyre developed an interest in the genotype to phenotype map. The emergence of new technologies for measuring gene expression, and the increasing availability of sequence data have provided motivation for her work on analytical approaches to modeling gene expression networks, and relating them to phenotypes. In 2006 Dr McIntyre moved to the University of Florida to join a campus wide Genetics Institute. She works on a wide variety of organisms, and remains interested in the fundamental question of the role of genetic variation.

Dr Lauren McIntyre, University of Florida, USA

Lauren McIntyre received her PhD in 1996 from North Carolina State University under the direction of Dr. Bruce Weir.Her PhD focused on testing Hardy-Weinberg Equilibrium.At Duke University Medical School she developed methods for mapping multigenic binary traits.In 1999, with a move to Purdue University, Dr. McIntyre developed an interest in the genotype to phenotype map.The emergence of new technologies for measuring gene expression,and the increasing availability of sequence data have provided motivation for her work on analytical approaches to modeling gene expression networks,and relating them to phenotypes.In 2006 Dr McIntyre moved to the University of Florida to join a campus wide Genetics Institute.She works on a wide variety of organisms, and remains interested in the fundamental question of the role of genetic variation.

High-dimensional QTL mapping in Arabidopsis

Professor Rebecca Doerge, Purdue University, USA

Abstract

Professor Rebecca Doerge joined Purdue University in 1995. She holds a joint appointment between the Colleges of Agriculture (Department of Agronomy) and Science (Department of Statistics). Professor Doerge's research program is focused on Statistical Bioinformatics, a component of bioinformatics that brings together many scientific disciplines into one arena to ask, answer, and disseminate biologically interesting information in the quest to understand the ultimate function of DNA and epigenomic associations for each and every genome. Rebecca has published over 100 scientific articles, published one book, and graduated over 17 Ph.D. students. She is an elected a Fellow of the American Statistical Association, a Fellow of the American Association for the Advancement of Science (AAAS), the Director of the Statistical Bioinformatics Center, and is currently the Head of the Department of Statistics, Purdue University.

Professor Rebecca Doerge, Purdue University, USA

Professor Rebecca Doerge joined Purdue University in 1995. She holds a joint appointment between the Colleges of Agriculture (Department of Agronomy) and Science (Department of Statistics). Professor Doerge's research program is focused on Statistical Bioinformatics, a component of bioinformatics that brings together many scientific disciplines into one arena to ask, answer, and disseminate biologically interesting information in the quest to understand the ultimate function of DNA and epigenomic associations for each and every genome. Rebecca has published over 100 scientific articles, published one book, and graduated over 17 Ph.D. students. She is an elected a Fellow of the American Statistical Association, a Fellow of the American Association for the Advancement of Science (AAAS), the Director of the Statistical Bioinformatics Center, and is currently the Head of the Department of Statistics, Purdue University.

Abstract

Enrico Petretto is a computational biologist with a proven track record and experience in statistical genetics, population genetics and genetic epidemiology applied to the study of complex traits and disease. He carried out his first studies in physical chemistry and then in statistical genetics, and in 2003 was awarded a PhD in Biochemistry, Biology and Molecular Biotechnologies at the University of Sassari in Italy. Now, he is Lecturer in Genomic Medicine at Imperial College London and group head at the MRC Clinical Science Centre where he leads the Integrative Genomics and Medicine Group. His group is highly interdisciplinary and aims to integrate genomics, informatics and multi-dimensional data modelling for the regulatory processes underlying complex traits, including metabolic, cardiovascular, inflammatory, neurological and behavioral phenotypes. In particular, rather than identifying single disease susceptibility genes affected by DNA variations, we are exploring pathways and networks (using reverse-engineering approaches) to predict the consequences of multiple genetic and epigenetic variants on complex disease.

Dr Enrico Petretto, Imperial College London, UK

Enrico Petretto is a computational biologist with a proven track record and experience in statistical genetics, population genetics and genetic epidemiology applied to the study of complex traits and disease. He carried out his first studies in physical chemistry and then in statistical genetics, and in 2003 was awarded a PhD in Biochemistry, Biology and Molecular Biotechnologies at the University of Sassari in Italy. Now, he is Lecturer in Genomic Medicine at Imperial College London and group head at the MRC Clinical Science Centre where he leads the Integrative Genomics and Medicine Group. His group is highly interdisciplinary and aims to integrate genomics, informatics and multi-dimensional data modelling for the regulatory processes underlying complex traits, including metabolic, cardiovascular, inflammatory, neurological and behavioral phenotypes. In particular, rather than identifying single disease susceptibility genes affected by DNA variations, we are exploring pathways and networks (using reverse-engineering approaches) to predict the consequences of multiple genetic and epigenetic variants on complex disease.

The genomics of human gene expression

Dr Barbara Stranger, Harvard Medical School, Harvard University, USA

Abstract

Barbara is currently Assistant Professor at Harvard Medical School and Brigham and Women’s hospital, where her lab focuses primarily on regulatory and population genomics in humans, from both healthy and diseased cohorts. She employs a combination of experimental and computational approaches designed to elucidate the identity, function, and evolutionary history of functional regions of the genome in order to gain a better understanding of the genetic and epigenetic basis of complex phenotypes. Current projects include integrative functional genomics of immune-cells of peripheral blood, as well projects specifically focusing on Preeclampsia, Asthma, and Multiple Sclerosis. She also has several collaborations involving regulatory genomics in model organisms Zebrafish and mouse. Her graduate and post-graduate training included positions in Montana, Germany, Spain, and the UK.

Dr Barbara Stranger, Harvard Medical School, Harvard University, USA

Barbara is currently Assistant Professor at Harvard Medical School and Brigham and Women’s hospital, where her lab focuses primarily on regulatory and population genomics in humans, from both healthy and diseased cohorts. She employs a combination of experimental and computational approaches designed to elucidate the identity, function, and evolutionary history of functional regions of the genome in order to gain a better understanding of the genetic and epigenetic basis of complex phenotypes. Current projects include integrative functional genomics of immune-cells of peripheral blood, as well projects specifically focusing on Preeclampsia, Asthma, and Multiple Sclerosis. She also has several collaborations involving regulatory genomics in model organisms Zebrafish and mouse. Her graduate and post-graduate training included positions in Montana, Germany, Spain, and the UK.

Dissecting quantitative resistance to rust in barley

Professor Robbie Waugh, Scottish Crop Research Institute, Dundee

Abstract

Robbie Waugh’s main research interests are in developing and applying genomics technologies to investigate the genetic control key traits in barley. Born in Glasgow in 1959, he obtained his undergraduate degree in Biology at the University of Strathclyde in 1981 before moving to Dundee where, in 1986, he obtained a PhD in Biochemistry and Molecular genetics from Dundee University. After a brief postdoc, in 1987 he took up a tenured position at SCRI, becoming the leader of the Genetics Department in 2005. He plays a significant role in national and international organisations that promote and co-ordinate global research on wheat and barley including the International Triticeae Mapping Initiative and the European Triticeae Genomics Initiative. He has published approaching 200 primary research articles in international peer reviewed journals. A current research aim is to exploit genetics to interrogate the complexity of the barley transcriptome and explore the use of transcript abundance in populations as a proxy for the dissection of complex traits.

Professor Robbie Waugh, Scottish Crop Research Institute, Dundee

Robbie Waugh’s main research interests are in developing and applying genomics technologies to investigate the genetic control key traits in barley. Born in Glasgow in 1959, he obtained his undergraduate degree in Biology at the University of Strathclyde in 1981 before moving to Dundee where, in 1986, he obtained a PhD in Biochemistry and Molecular genetics from Dundee University. After a brief postdoc, in 1987 he took up a tenured position at SCRI, becoming the leader of the Genetics Department in 2005. He plays a significant role in national and international organisations that promote and co-ordinate global research on wheat and barley including the International Triticeae Mapping Initiative and the European Triticeae Genomics Initiative. He has published approaching 200 primary research articles in international peer reviewed journals. A current research aim is to exploit genetics to interrogate the complexity of the barley transcriptome and explore the use of transcript abundance in populations as a proxy for the dissection of complex traits.

Causally cohesive genotype-to-phenotype maps

Dr Stig Omholt, Centre for Integrative Genetics, Norwegian University of Life Sciences, Norway

Abstract

Dr Stig W Omholt is Professor at the Norwegian University of Life Sciences and Director of its Centre for Integrative Genetics, Ås, Norway. He is currently Kristine Bonnevie Professor at the Centre for Ecological and Evolutionary Synthesis at the University of Oslo, Norway. His research background includes theoretical and experimental work on honeybees to elucidate sociobiological and biogerontologcal phenomena, the provision of mathematical frameworks to understand gene regulatory networks, functional genomics on salmonids, and elucidation of genetic concepts by use of genetic network modelling. His research is now focused on linking genetics theory and methodology to multi-scale modelling of complex physiological systems to understand genotype–phenotype map relationships.

Dr Stig Omholt, Centre for Integrative Genetics, Norwegian University of Life Sciences, Norway

Dr Stig Omholt, Centre for Integrative Genetics, Norwegian University of Life Sciences, Norway

Membership status unknown

No primary institution

Dr Stig W Omholt is Professor at the Norwegian University of Life Sciences and Director of its Centre for Integrative Genetics, Ås, Norway. He is currently Kristine Bonnevie Professor at the Centre for Ecological and Evolutionary Synthesis at the University of Oslo, Norway. His research background includes theoretical and experimental work on honeybees to elucidate sociobiological and biogerontologcal phenomena, the provision of mathematical frameworks to understand gene regulatory networks, functional genomics on salmonids, and elucidation of genetic concepts by use of genetic network modelling. His research is now focused on linking genetics theory and methodology to multi-scale modelling of complex physiological systems to understand genotype–phenotype map relationships.

Abstract

Dr Krishnan gained her medical degree in 2007, and was awarded a Kennedy Memorial scholarship to spend a year as a Research Fellow at Harvard Medical School. She is currently an Academic Clinical Fellow in Neonatology at Imperial College London. Her research involves inter-disciplinary approaches to clinical neuroscience questions. This draws from the fields of integrative genomics, imaging and systems biology.

Recently she joined the Integrative Genomics and Medicine group at the Medical Research Council Clinical Sciences Centre with Dr Enrico Petretto. Their work explores gene networks involved in epilepsy, using live human tissue from a cohort of patients with drug-resistant focal epilepsy.

Previous work focused on computational radiology approaches to neurodevelopmental disorders including tuberous sclerosis and consequences of preterm birth. She has published work with Professor David Edwards at the Centre for the Developing Brain, Imperial College, and with Professor Simon Warfield at the Computational Radiology Laboratory, Harvard Medical School.

Dr Michelle Krishnan, Imperial College London, UK

Dr Krishnan gained her medical degree in 2007, and was awarded a Kennedy Memorial scholarship to spend a year as a Research Fellow at Harvard Medical School.She is currently an Academic Clinical Fellow in Neonatology at Imperial College London. Her research involves inter-disciplinary approaches to clinical neuroscience questions.This draws from the fields of integrative genomics, imaging and systems biology.

Recently she joined the Integrative Genomics and Medicine group at the Medical Research Council Clinical Sciences Centre with Dr Enrico Petretto.Their work explores gene networks involved in epilepsy, using live human tissue from a cohort of patients with drug-resistant focal epilepsy.

Previous work focused on computational radiology approaches to neurodevelopmental disorders including tuberous sclerosis and consequences of preterm birth.She has published work with Professor David Edwards at the Centre for the Developing Brain, Imperial College, and with Professor Simon Warfield at the Computational Radiology Laboratory, Harvard Medical School.

Abstract

Ana Viñuela was born in Madrid, Spain. After graduating in Biology (BSc), she specialized in Genetics (MSc) at the Complutense University of Madrid, Spain. She completed her studies with a Master in Bioinformatics and Computational Biology. As part of her studies, she attended lectures at the Friedrich-Schiller-Universität of Jena, Germany with an Erasmus scholarship. Also, she completed a four months internship program at the Center for Biological Sequence Analysis at the Denmark Technical University, Denmark. In February 2007 she was appointed as PhD student with Dr Ing Jan E Kammenga at the Laboratory of Nematology at Wageningen University, The Netherlands. In March 2011 she received her PhD degree for her studies in the genetic architecture of gene expression in the nematode Caenorhabditis elegans. She is one of the winners of the GENESYS travel award.

Dr Ana Vinuela, Laboratory of Nematology, Netherlands

Ana Viñuela was born in Madrid, Spain. After graduating in Biology (BSc), she specialized in Genetics (MSc) at the Complutense University of Madrid, Spain. She completed her studies with a Master in Bioinformatics and Computational Biology. As part of her studies, she attended lectures at the Friedrich-Schiller-Universität of Jena, Germany with an Erasmus scholarship. Also, she completed a four months internship program at the Center for Biological Sequence Analysis at the Denmark Technical University, Denmark. In February 2007 she was appointed as PhD student with Dr Ing Jan E Kammenga at the Laboratory of Nematology at Wageningen University, The Netherlands. In March 2011 she received her PhD degree for her studies in the genetic architecture of gene expression in the nematode Caenorhabditis elegans. She is one of the winners of the GENESYS travel award.